Update member variable names to avoid shadowing (#102)

* Update Channel.hpp/cpp to avoid shadowing * Fix formatting * Update names in RecordingContainers * Update members in NWBFile * Update members in Container * Fix formatting * Update members in Data.hpp * Update member in HDF5RecordingData * Update members in BaseIO and HDF5IO * Update members in VectorData * Fix formatting * Fix ubuntu build error * Fix Doxygen built errors * Replace this->m_ with just m_ * Update src/nwb/ecephys/SpikeEventSeries.hpp Co-authored-by: Steph Prince <[email protected]> * Remove setters from channel * Make simple getters in BaseIO in the header and remove redundant override of getFilename in HDF5IO * Fix formatting * Make simple getter for HDF5RecordingData inline * Make simple getter for RecordingContainers inline * replace this->m_ with just m_ * Move simple setters for DynamicTable and remove redundant definitions with ElectrodeTable * fix formatting * Fix formatting * Move VectorData getters * Fix hidden ElectrodeTable.colNames member and bad init --------- Co-authored-by: Steph Prince <[email protected]>
NeurodataWithoutBorders · Sep 20, 2024 · 33e3481 · 33e3481
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diff --git a/docs/pages/userdocs/workflow.dox b/docs/pages/userdocs/workflow.dox
@@ -8,94 +8,94 @@
  * For users wanting to integrate NWB with a particular data acquisition software, here
  * we outline the steps for a single recording from file creation to saving.
  *
- * 1. Create the I/O object (e.g,.  \ref AQNWB::HDF5::HDF5IO "HDF5IO") used for 
+ * 1. Create the I/O object (e.g,.  \ref AQNWB::HDF5::HDF5IO "HDF5IO") used for
  *    writing data to the file on disk.
- * 2. Create the \ref AQNWB::NWB::RecordingContainers "RecordingContainers" object 
+ * 2. Create the \ref AQNWB::NWB::RecordingContainers "RecordingContainers" object
  *    used for managing \ref AQNWB::NWB::Container "Container" objects for storing recordings.
- * 3. Create the \ref AQNWB::NWB::NWBFile "NWBFile" object used for managing and creating NWB 
+ * 3. Create the \ref AQNWB::NWB::NWBFile "NWBFile" object used for managing and creating NWB
  *    file contents.
- * 4. Create the \ref AQNWB::NWB::Container "Container" objects (e.g., 
- *    \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries") used for recording and add them 
+ * 4. Create the \ref AQNWB::NWB::Container "Container" objects (e.g.,
+ *    \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries") used for recording and add them
  *    to the \ref AQNWB::NWB::RecordingContainers "RecordingContainers".
  * 5. Start the recording.
  * 6. Write data.
  * 7. Stop the recording and close the \ref AQNWB::NWB::NWBFile "NWBFile".
- * 
+ *
  * Below, we walk through these steps in more detail.
- * 
- * 
+ *
+ *
  * \subsection create_io 1. Create the I/O object.
- * 
- * First, create an I/O object (e.g., \ref AQNWB::HDF5::HDF5IO "HDF5IO") used for writing 
+ *
+ * First, create an I/O object (e.g., \ref AQNWB::HDF5::HDF5IO "HDF5IO") used for writing
  * data to the file. AqNWB provides the convenience method, \ref AQNWB::createIO "createIO"
  * to create this object using one of the supported backends. For more fine-grained
- * control of different backend parameters, you can create your own `std::shared_ptr` 
+ * control of different backend parameters, you can create your own `std::shared_ptr`
  * using any of the derived \ref AQNWB::BaseIO "BaseIO" classes.
- * 
+ *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_io_snippet
  *
  *
  * \subsection create_recording_container 2. Create the RecordingContainer object.
- * 
- * Next, create a \ref AQNWB::NWB::RecordingContainers "RecordingContainers"  object to manage the 
- * different \ref AQNWB::NWB::Container "Container" objects with the datasets that you would 
+ *
+ * Next, create a \ref AQNWB::NWB::RecordingContainers "RecordingContainers"  object to manage the
+ * different \ref AQNWB::NWB::Container "Container" objects with the datasets that you would
  * like to write data to.
- * 
+ *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_recording_containers_snippet
- * 
+ *
  *
  * \subsection create_nwbfile 3. Create the NWBFile
- * 
- * Next, constructs the \ref AQNWB::NWB::NWBFile "NWBFile"  object, using the I/O object as an input. 
+ *
+ * Next, constructs the \ref AQNWB::NWB::NWBFile "NWBFile"  object, using the I/O object as an input.
  * Then, initialize the object to create the basic file structure of the NWBFile.
  *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_nwbfile_snippet
  *
- * 
+ *
  * \subsection create_datasets 4. Create datasets and add to RecordingContainers.
  *
- * Next, create the different data types (e.g. \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries" 
- * or other AQNWB::NWB::TimeSeries "TimeSeries") that you would like to write data into. After 
- * creation, these objects are added to the  \ref AQNWB::NWB::RecordingContainers "RecordingContainers"  
- * object so that it can mana ge access and data writing during the recording process. 
- * When adding containers, ownership of the \ref AQNWB::NWB::Container "Container"  is transferred to the 
- * \ref AQNWB::NWB::RecordingContainers "RecordingContainers" object, so that we can access it again via 
- * its index. New containers will always be appended to the end of the
- * \ref AQNWB::NWB::RecordingContainers::containers "containers" object and their index can be tracked 
- * using the size of the input `recordingArrays`.
- * 
+ * Next, create the different data types (e.g. \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries"
+ * or other AQNWB::NWB::TimeSeries "TimeSeries") that you would like to write data into. After
+ * creation, these objects are added to the  \ref AQNWB::NWB::RecordingContainers "RecordingContainers"
+ * object so that it can mana ge access and data writing during the recording process.
+ * When adding containers, ownership of the \ref AQNWB::NWB::Container "Container"  is transferred to the
+ * \ref AQNWB::NWB::RecordingContainers "RecordingContainers" object, so that we can access it again via
+ * its index. New containers will always be appended to the end of the private member
+ * ``RecordingContainers.m_containers` object and their index can be tracked
+ * using the \ref AQNWB::NWB::RecordingContainers::size "RecordingContainers.size" of the input `recordingArrays`.
+ *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_datasets_snippet
  *
  *
  * \subsection start_recording 5. Start the recording.
  *
- * Then, start the recording process with a call to the ``startRecording`` function of the I/O object. 
+ * Then, start the recording process with a call to the ``startRecording`` function of the I/O object.
  *
- *  \note 
- * When using \ref AQNWB::HDF5::HDF5IO "HDF5IO" for writing to HDF5, calling 
+ *  \note
+ * When using \ref AQNWB::HDF5::HDF5IO "HDF5IO" for writing to HDF5, calling
  * \ref AQNWB::HDF5::HDF5IO::startRecording "startRecording" will by default enable
- * \ref hdf5io_swmr "SWMR mode" to ensure file integrity and support concurrent read. 
+ * \ref hdf5io_swmr "SWMR mode" to ensure file integrity and support concurrent read.
  * As a result, no additional datasets or groups can be added to the file once a recording
  * has been started unless the file is is closed and reopened.
  *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_start_snippet
  *
- * 
+ *
  * \subsection write_data 6. Write data.
  *
- * During the recording process, use the \ref AQNWB::NWB::RecordingContainers "RecordingContainers" 
- * as an interface to access the various  \ref AQNWB::NWB::Container "Container" object and corresponding 
- * datasets and write blocks of data to the file. Calling `flush()` on the I/O object at any time will 
+ * During the recording process, use the \ref AQNWB::NWB::RecordingContainers "RecordingContainers"
+ * as an interface to access the various  \ref AQNWB::NWB::Container "Container" object and corresponding
+ * datasets and write blocks of data to the file. Calling `flush()` on the I/O object at any time will
  * ensure the data is moved to disk.
- * 
+ *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_write_snippet
  *
- * 
+ *
  * \subsection stop_recording 7. Stop the recording and finalize the file.
  *
  * When the recording process is finished, call `stopRecording` from the I/O object
  * to flush any data and close the file.
- * 
+ *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_stop_snippet
  *
  *

diff --git a/src/BaseIO.cpp b/src/BaseIO.cpp
@@ -31,29 +31,15 @@ const BaseDataType BaseDataType::DSTR = BaseDataType(T_STR, DEFAULT_STR_SIZE);
 
 // BaseIO
 
-BaseIO::BaseIO()
-    : readyToOpen(true)
-    , opened(false)
+BaseIO::BaseIO(const std::string& filename)
+    : m_filename(filename)
+    , m_readyToOpen(true)
+    , m_opened(false)
 {
 }
 
 BaseIO::~BaseIO() {}
 
-bool BaseIO::isOpen() const
-{
-  return opened;
-}
-
-bool BaseIO::isReadyToOpen() const
-{
-  return readyToOpen;
-}
-
-bool BaseIO::canModifyObjects()
-{
-  return true;
-}
-
 Status BaseIO::createCommonNWBAttributes(const std::string& path,
                                          const std::string& objectNamespace,
                                          const std::string& neurodataType,

diff --git a/src/BaseIO.hpp b/src/BaseIO.hpp
@@ -94,7 +94,7 @@ class BaseIO
   /**
    * @brief Constructor for the BaseIO class.
    */
-  BaseIO();
+  BaseIO(const std::string& filename);
 
   /**
    * @brief Copy constructor is deleted to prevent construction-copying.
@@ -115,7 +115,7 @@ class BaseIO
    * @brief Returns the full path to the file.
    * @return The full path to the file.
    */
-  virtual std::string getFileName() = 0;
+  virtual std::string getFileName() const { return m_filename; }
 
   /**
    * @brief Opens the file for writing.
@@ -267,7 +267,7 @@ class BaseIO
    * override this function to check if objects can be modified.
    * @return True if the file is in a modification mode, false otherwise.
    */
-  virtual bool canModifyObjects();
+  virtual bool canModifyObjects() { return true; }
 
   /**
    * @brief Creates an extendable dataset with a given base data type, size,
@@ -338,20 +338,20 @@ class BaseIO
    * @brief Returns true if the file is open.
    * @return True if the file is open, false otherwise.
    */
-  bool isOpen() const;
+  inline bool isOpen() const { return m_opened; }
 
   /**
    * @brief Returns true if the file is able to be opened.
    * @return True if the file is able to be opened, false otherwise.
    */
-  bool isReadyToOpen() const;
+  inline bool isReadyToOpen() const { return m_readyToOpen; }
 
+protected:
   /**
    * @brief The name of the file.
    */
-  const std::string filename;
+  const std::string m_filename;
 
-protected:
   /**
    * @brief Creates a new group if it does not already exist.
    * @param path The location of the group in the file.
@@ -362,12 +362,12 @@ class BaseIO
   /**
    * @brief Whether the file is ready to be opened.
    */
-  bool readyToOpen;
+  bool m_readyToOpen;
 
   /**
    * @brief Whether the file is currently open.
    */
-  bool opened;
+  bool m_opened;
 };
 
 /**

diff --git a/src/Channel.cpp b/src/Channel.cpp
@@ -14,32 +14,17 @@ Channel::Channel(const std::string name,
                  const float bitVolts,
                  const std::array<float, 3> position,
                  const std::string comments)
-    : name(name)
-    , groupName(groupName)
-    , groupIndex(groupIndex)
-    , localIndex(localIndex)
-    , globalIndex(globalIndex)
-    , position(position)
-    , conversion(conversion)
-    , samplingRate(samplingRate)
-    , bitVolts(bitVolts)
-    , comments(comments)
+    : m_name(name)
+    , m_groupName(groupName)
+    , m_groupIndex(groupIndex)
+    , m_localIndex(localIndex)
+    , m_globalIndex(globalIndex)
+    , m_position(position)
+    , m_conversion(conversion)
+    , m_samplingRate(samplingRate)
+    , m_bitVolts(bitVolts)
+    , m_comments(comments)
 {
 }
 
 Channel::~Channel() {}
-
-float Channel::getConversion() const
-{
-  return bitVolts / conversion;
-}
-
-float Channel::getSamplingRate() const
-{
-  return samplingRate;
-}
-
-float Channel::getBitVolts() const
-{
-  return bitVolts;
-}